The Nielsen Lab has developed several software packages including:

BALLET
A program for scanning genomic data for balancing selection. Written by Mike DeGiorgio, now at Penn State. Learn more here.
ANGSD
Analyses of Next Generation Sequencing Data. Our new program package for analyzing NGS data developed by Thorfinn Korneliusen with help from Anders Albrechtsen and others. Learn more here.
nSL
nSL is a program for efficiently computing the nSL statistic described in Ferrer et al. 2014. Learn more here.
ngsTools
C/C++ programs to simulate NGS data, to compute estimates of FST, of the sample covariance matrix and of the 2D-SFS, by Matteo Fumagalli. Estimates of population genetics parameters are based on posterior probabilities of genotypes and sample allele frequencies as in Nielsen et al. 2012. Input files can be generated using the ANGSD software. Learn more here.
ngsF
A program to estimate per-individual inbreeding coefficients by Filippe Vieira. Learn more here
SweepFinder2
It can be used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data. Learn more here.
trueFS
Used for finding the ascertainment corrected frequency spectrum based on ascertained SNP data. Learn more here.
codonbias
Program will allow the user to estimate selection coefficients relating to optimal codon usage. Learn more here.
CodonRecSim
A program for simulating samples in a codon based models under the coalescent with recombination. Learn more here.
PATRI
(PaTeRnity Inference) A program for paternity analysis of genetic data. Learn more here.
IM and IMa
IM and IMa set of programs for estimating migration rates, divergence times, and effective population sizes were developed in collaboration with Jody Hey’s group. Learn more here.
MDIV
A program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). For most purposes you probably want to use one of the IM programs instead. Learn more here.
BAMSE
A phenomenal, and terribly underutilized, program developed by Anders Albrechtsen. It provides a very flexible method for association mapping for multifactorial traits in the presence of gene-gene and gene-environment interactions. I have really no idea why this method is not more used in association mapping studies – but I guess we can’t be too great at advertising. Learn more here.
Relate
An R package for estimating pair wise relatedness using maximum likelihood for genome-wide data while taking LD into account. This is another program by Anders Albrechtsen. Learn more here.
MISAT
A program for estimating the likelihood surface for theta (4 times the effective population size times the mutation rate) for population genetic microsatellite data. This program is old. There must be better methods out there. Learn more here.
MCMC_IBDfinder
An MCMC program by Ida Moltke for estimating posterior probabilities of identity by descent (IBD) sharing between multiple individuals using unphased single nucleotide polymorphism (SNP) data. Learn more here.
AssotesteR
An R package by Gaston Sanchez with statistical tests and methods for genetic association studies with emphasis on rare variants and binary (dichotomous) traits. Learn more here.

Browse additional programs made available by the Center for Theoretical Evolutionary Genomics here.